Recent changes to Developers.Variables.intra

Developers.Variables.intra modified by Burkhard Schmidt

Burkhard Schmidt — Mon, 17 Jun 2013 11:58:08 -0000

--- v21
+++ v22
@@ -29,9 +29,9 @@

 field | description
 ---|---
-thawed | table of interaction energies of thawed molecules
+thawed | table of interaction energies inside thawed molecules

-Note that this table is needed for efficient evaluation of gradient and Hessian of the intramolecular force field. Interaction within frozen molecules is disregarded.
+Note that this table is needed for efficient evaluation of gradient and Hessian of the intramolecular force field. Interaction inside frozen molecules is disregarded.

 Write your own intramolecular force field:

Developers.Variables.intra modified by Burkhard Schmidt

Burkhard Schmidt — Mon, 17 Jun 2013 10:26:35 -0000

--- v20
+++ v21
@@ -31,7 +31,7 @@
 ---|---
 thawed | table of interaction energies of thawed molecules

-Note that this table is needed for efficient evaluation of gradient and Hessian. Interaction within frozen molecules is disregarded.
+Note that this table is needed for efficient evaluation of gradient and Hessian of the intramolecular force field. Interaction within frozen molecules is disregarded.

 Write your own intramolecular force field:

Developers.Variables.intra modified by Burkhard Schmidt

Burkhard Schmidt — Mon, 10 Jun 2013 10:03:39 -0000

--- v19
+++ v20
@@ -17,7 +17,7 @@
 r_e | position of minimum (in nm)
 alf | range parameter (inverse length, in 1/nm)

-[@ff1.Harmonic](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff1/Harmonic.m) | harmonic force field (so far only for bent ABA triatomics) 
+[@ff1.Harmonic](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff1/Harmonic.m) | harmonic force field (so far only for bent ABA triatomics, e.g., H2O) 
 ---|---
 r_0 | equilibrium bond length, in nm
 a_0 | equilibrium bond angle, in rad
@@ -29,7 +29,9 @@

 field | description
 ---|---
-thawed | table of interaction energies of thawed molecules; needed for efficient evaluation of gradient and Hessian
+thawed | table of interaction energies of thawed molecules
+
+Note that this table is needed for efficient evaluation of gradient and Hessian. Interaction within frozen molecules is disregarded.

 Write your own intramolecular force field:

Developers.Variables.intra modified by Burkhard Schmidt

Burkhard Schmidt — Mon, 10 Jun 2013 08:43:13 -0000

--- v18
+++ v19
@@ -1,7 +1,7 @@
 Variable "intra{.}" in MolDynSim
 ==================================

-This variable characterizes the intramolecular force fields for each molecular species in our simulations. It is used in essentially all of the MolDynSim programs. Every entry of the cell vector is a structured variable that containing the following
+This variable characterizes the intramolecular force fields for each molecular species in our simulations. It is used in essentially all of the MolDynSim programs. Every entry of the cell vector is a structured variable that containing the following items

 Settable parameters
 -------------------
@@ -25,8 +25,14 @@
 k_a | bending force constant, in kJ/(mol*rad^2)

 Internal variables
+------------------

-Write your own force field: 
----------------------------
+field | description
+---|---
+thawed | table of interaction energies of thawed molecules; needed for efficient evaluation of gradient and Hessian
+
+
+Write your own intramolecular force field: 
+------------------------------------------

 * If you cannot find a suitable function inside the +ff1 package, you will have to provide one yourself. For a guide how to write an intramolecular force field, please see [here](Developers.ForceFields.intra).

Developers.Variables.intra modified by Burkhard Schmidt

Burkhard Schmidt — Mon, 10 Jun 2013 08:38:49 -0000

--- v17
+++ v18
@@ -1,7 +1,10 @@
 Variable "intra{.}" in MolDynSim
 ==================================

-This variable characterizes the intramolecular force fields for each molecular species in our simulations. It is used in essentially all of the MolDynSim programs. Every entry of the cell vector is a structured variable that should contain the following two fields:
+This variable characterizes the intramolecular force fields for each molecular species in our simulations. It is used in essentially all of the MolDynSim programs. Every entry of the cell vector is a structured variable that containing the following
+
+Settable parameters
+-------------------

 field | description
 ---|---
@@ -21,6 +24,8 @@
 k_r | stretching force constant, in kJ/(mol*nm^2)
 k_a | bending force constant, in kJ/(mol*rad^2)

+Internal variables
+
 Write your own force field: 
 ---------------------------

Developers.Variables.intra modified by Burkhard Schmidt

Burkhard Schmidt — Mon, 10 Jun 2013 07:12:44 -0000

--- v16
+++ v17
@@ -1,12 +1,12 @@
-Variable "intra{i}" in MolDynSim
+Variable "intra{.}" in MolDynSim
 ==================================

-This variable characterizes the intramolecular force fields for the *i*-th molecular species in our simulations. It is used in essentially all of the MolDynSim programs. Every entry *{i}* of the cell vector is a structured variable that should contain the following two fields:
+This variable characterizes the intramolecular force fields for each molecular species in our simulations. It is used in essentially all of the MolDynSim programs. Every entry of the cell vector is a structured variable that should contain the following two fields:

 field | description
 ---|---
 handle | choice of force field to be used (MATLAB function handle, see below); normally found in +ff1 package
-parameter | structure containing all necessary parameters, depending on the choice of the function handle, see below
+parameter | structure containing all necessary parameters, depending on the choice of the function handle, see the following lists

 [@ff1.Morse](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff1/Morse.m) | anharmonic Morse oscillator (so far only for diatomics) 
 ---|---

Developers.Variables.intra modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 06 Jun 2013 12:40:25 -0000

--- v15
+++ v16
@@ -5,7 +5,7 @@

 field | description
 ---|---
-handle | choice of potential function to be used (MATLAB function handle, see below)
+handle | choice of force field to be used (MATLAB function handle, see below); normally found in +ff1 package
 parameter | structure containing all necessary parameters, depending on the choice of the function handle, see below

 [@ff1.Morse](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff1/Morse.m) | anharmonic Morse oscillator (so far only for diatomics) 
@@ -14,6 +14,13 @@
 r_e | position of minimum (in nm)
 alf | range parameter (inverse length, in 1/nm)

+[@ff1.Harmonic](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff1/Harmonic.m) | harmonic force field (so far only for bent ABA triatomics) 
+---|---
+r_0 | equilibrium bond length, in nm
+a_0 | equilibrium bond angle, in rad
+k_r | stretching force constant, in kJ/(mol*nm^2)
+k_a | bending force constant, in kJ/(mol*rad^2)
+
 Write your own force field: 
 ---------------------------

Developers.Variables.intra modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 06 Jun 2013 12:24:11 -0000

--- v14
+++ v15
@@ -10,9 +10,9 @@

 [@ff1.Morse](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff1/Morse.m) | anharmonic Morse oscillator (so far only for diatomics) 
 ---|---
-d_e : dissociation energy (well depth, in kJ/mol)
-r_e : position of minimum (in nm)
-alf : range parameter (inverse length, in 1/nm)
+d_e | dissociation energy (well depth, in kJ/mol)
+r_e | position of minimum (in nm)
+alf | range parameter (inverse length, in 1/nm)

 Write your own force field: 
 ---------------------------

Developers.Variables.intra modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 06 Jun 2013 12:23:11 -0000

--- v13
+++ v14
@@ -8,6 +8,12 @@
 handle | choice of potential function to be used (MATLAB function handle, see below)
 parameter | structure containing all necessary parameters, depending on the choice of the function handle, see below

+[@ff1.Morse](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff1/Morse.m) | anharmonic Morse oscillator (so far only for diatomics) 
+---|---
+d_e : dissociation energy (well depth, in kJ/mol)
+r_e : position of minimum (in nm)
+alf : range parameter (inverse length, in 1/nm)
+
 Write your own force field: 
 ---------------------------

Developers.Variables.intra modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 06 Jun 2013 11:48:33 -0000

--- v12
+++ v13
@@ -1,14 +1,14 @@
 Variable "intra{i}" in MolDynSim
 ==================================

-This variable characterizes the intramolecular force fields for the *i*-th molecular species in our simulations. It is used in essentially all of the MolDynSim programs. Every entry *{i}* of the cell vector is a structured variable that should initially contain the following fields:
+This variable characterizes the intramolecular force fields for the *i*-th molecular species in our simulations. It is used in essentially all of the MolDynSim programs. Every entry *{i}* of the cell vector is a structured variable that should contain the following two fields:

 field | description
 ---|---
-handle | choice of potential function to be used (MATLAB function handle)
+handle | choice of potential function to be used (MATLAB function handle, see below)
 parameter | structure containing all necessary parameters, depending on the choice of the function handle, see below

 Write your own force field: 
 ---------------------------

-* If you cannot find a suitable potential function inside the +ff1 function package, you will have to  provide one yourself. For a guide how to write an intramolecular potential function, please see [here](Developers.ForceFields.intra).
+* If you cannot find a suitable function inside the +ff1 package, you will have to provide one yourself. For a guide how to write an intramolecular force field, please see [here](Developers.ForceFields.intra).